User:Adithya Sagar/Sandbox DNA



Double Helix
DNA consists of two polynucleotide chains, twisted around each other to form a double helix. The nucleotide in DNA is composed of of a 5' phosphorylated sugar, beta-D-2'- deoxyribose and a purine or a pyrimidine base. The four types of bases are the two double ringed purine base Adenine (A) and Guanine (G) and the two single pyrimidine bases Thymine (T) and Cytosine (C). Each nucleotide in a DNA chain is linked to another via 3',5' phosphodiester bond. There are four nucleotides in DNA. The sugar-phosphate backbone of the DNA is very regular owing the phosphodiester linkage whereas the ordering of bases is highly irregular.

Complementary Bases
The two chains in a DNA are joined by hydrogen bonds between specific bases. Adenine forms a base pairs with Thymine and Guanine with Cytosine. This specific base pairing between Adenine-Thymine and Guanine-Cytosine is known as Watson-Crick base pairing. The specificity of hydrogen bonding between bases leads to complementarity in the sequence of nucleotides in the two chains. Thus in a strand of DNA the content of Adenine is equal to that of Thymine and the Guanine content is equal to the cytosine content. In general DNA with higher GC content is more stable than the one with higher AT content owing to the stabilization due to base stacking interactions.

DNA denaturation and renaturation
A DNA double strand can be separated into two single strands by breaking the hydrogen bonds between them. This is known as DNA denaturation. Thermal energy provided by heating can be used to melt or denature DNA. Molecules with rich GC content are more stable and thus denature at higher temperatures compared to the ones with higher AT content. The melting temperature is defined as the temperature at which half the DNA strands are in double helical state and half are in random coil state. [Santa Lucia -chk. The denatured DNA single strands have an ability to renature and form double stranded DNA again.

Grooves
In a DNA double helix the beta-glycosyl bonds between C1'- N1 branch off from one side of the base pair and do not lie opposite to each other. This results in unequally spaced sugar-phosphate backbones and gives rise to two grooves of different width and depth. The minor groove is at the O2 side of base pair and the major groove is on the opposite side [Saenger]. The floor of major groove is filled with nitrogen and oxygen atoms that project inward whereas in the minor groove they project outward. The larger size of major groove allows for the binding of DNA specific proteins.

Tautomeric forms of bases
The hydrogen atoms on the bases move from nitrogen or oxygen atom on ring to another through shifts known as tautomeric shits. However the hydrogens have preferred atomic locations. Based on the movement of hydrogen atoms the nitrogen atoms are in amino or imino configuration and the oxygen atoms are either in keto or enol forms. However there is a preference for the amino and keto forms respectively. This is very crucial for the biological functioning of DNA as this preference leads to the specificity in base pairing and thus complementarity of the chains.

Forms of DNA
See Also: Z-DNA

  

 A    sync jmolAppletB,jmolAppletZ  sync OFF Synchronize 

DNA is a very flexible molecule and has the ability to exist in various forms based on the environmental conditions. Naturally occurring DNA double helices are classified into A, B and Z-types. A and B-forms of DNA are the right handed forms whereas Z-DNA is the left handed form. When hydrated the DNA generally assumes B-form. The A conformation is found when there is little water to interact with the helix. The formation of Z-DNA occurs with the methylation of deoxycytosine residues and also during transcription where negative supercoiling stabilizes it.

Replication
DNA undergoes what is known as semi conservative mode of replication wherein the daughter DNA contains one DNA strand of the parent. The replication can be explained in the following stages.

Unwinding of parental DNA
The supercoiled duplex DNA unwinds with the aid of several proteins. DNA helicase promotes the unwinding by binding to the single-stranded DNA. This followed by the negative supercoiling of DNA by DNA gyrase which lowers the the energy required to disrupt a base pair. Another helicase called the rep protein also helps in the denaturation of DNA by disrupting the base pairs.

Synthesis of an Oligonucleotide primer
The unwinding of DNA is followed by the binding of protein dnaB at the origin of replication of DNA and remains bound to the replication fork. This binding acts as a signal for a protein called primase an RNA polymerase which synthesizes a short complementary strand at the origin of replication.

Discontinuous synthesis at the Replication fork
The elongation of the primer on the template strands is done by an enzyme known as DNA polymerase. Synthesis of complementary DNA occurs simultaneously on both the parent strands. However the synthesis occurs from 5'-3' continuously on only one strand called the leading strand. On the other strand known as lagging strand chain growth occurs discontinuously. Short strands of polynucleotides known as Okazaki fragments are formed complementary to the lagging strand.

Primer Excision and Phosphodiester bond formation
In this step a ribonuclease removes the RNA primer, the DNA polymerase fills the gap and DNA ligase fills the nicks between the DNA fragments.

Transcription and Translation
The expression of genes into proteins and is a process involving two stages called transcription and translation. In the transcription stage a strand of DNA molecule serves as a template for the synthesis of an RNA molecule called messenger RNA. This messenger RNA is then translated into proteins on ribosomes. The transcription step that involves the synthesis of mRNA from can explained in the following stages.

RNA polymerase binding to specific site on double-helical DNA
The RNA polymerase of prokaryotes is an oligomer composed of fice subunits arranged in an oligomer known as core enzyme. A sixth subunit called sigma subunit binds to core enzyme to give the holoenzyme. This enyme is responsible for binding RNA polymerase holoenzyme to specific transcritption sites on DNA. In eukaryotes there are three types of RNA polymerases called RNA polymerase 1,2 and 3 which synthesize different types of RNA.

Synthesis of RNA
There are many binding sites on DNA for RNA polymerase. Binding at certain sites is stronger than the rest and causes the initiation of RNA synthesis. These sites are known as promoter regions. In general these regions contain the following sequence

5'TATPuATG3' 3'ATAPyTAC5'

The binding is followed by the separation of DNA strands and synthesis of RNA by RNA polymerase.

Termination of Transcription
Specific DNA sequences rich in T followed by G-C rich sequences are responsible for termination of transcription. When RNA polymerase reaches these T rich sequences it pauses and the synthesized RNA is released. The termination process is aided by a protein called rho factor. It binds to RNA polymerase, RNA and DNA at the pause signal and RNA is released.

Transformation between A-B DNA
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